MolNFT v1 · #65139 · protein + DNA
Mutm encountering an intrahelical 8-oxoguanine (oxog) lesion in EC3- loop deletion complex
3GO8 · Formamidopyrimidine-DNA glycosylase: “Mutm encountering an intrahelical 8-oxoguanine (oxog) lesion in EC3- loop deletion complex”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.64). MolNFT v1 #65139 on GenesisL1…
- PDB
- 3GO8
- Type
- protein + DNA
- Length
- 280 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidine-DNA glycosylase; 5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*G)-3'…
- EC
- 3.2.2.23, 4.2.99.18
- UniProt
- P84131
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23, 4.2.99.18) | protein | 252 | 31% helix, 26% strand | P84131 |
| B | 5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*G)-3' | dna | 14 | — | — |
| C | 5'-D(*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*C)-3' | dna | 14 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.64 | 0.78 | 38 | empty |
| 2 | 130 | 0.46 | 0.79 | 20 | empty |
| 3 | 121 | 0.36 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 668 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 660 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–B · 419 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3GO8 · MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC3-loop deletion complex · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P84131
- Elsewhere: RCSB PDB 3GO8 · PDBe 3GO8 · UniProt P84131
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